[2024-01-24 12:21:41,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:41,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:41,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg64e76f14-ddfb-470b-a1b9-e717f2a759e1/dqc_reference
[2024-01-24 12:21:42,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:42,918] [INFO] Task started: Prodigal
[2024-01-24 12:21:42,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg657873f8-a702-49e9-9cb1-5cfdedff89c8/GCF_004342005.1_ASM434200v1_genomic.fna.gz | prodigal -d GCF_004342005.1_ASM434200v1_genomic.fna/cds.fna -a GCF_004342005.1_ASM434200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:55,151] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:55,152] [INFO] Task started: HMMsearch
[2024-01-24 12:21:55,152] [INFO] Running command: hmmsearch --tblout GCF_004342005.1_ASM434200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64e76f14-ddfb-470b-a1b9-e717f2a759e1/dqc_reference/reference_markers.hmm GCF_004342005.1_ASM434200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:55,479] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:55,481] [INFO] Found 6/6 markers.
[2024-01-24 12:21:55,532] [INFO] Query marker FASTA was written to GCF_004342005.1_ASM434200v1_genomic.fna/markers.fasta
[2024-01-24 12:21:55,532] [INFO] Task started: Blastn
[2024-01-24 12:21:55,532] [INFO] Running command: blastn -query GCF_004342005.1_ASM434200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64e76f14-ddfb-470b-a1b9-e717f2a759e1/dqc_reference/reference_markers.fasta -out GCF_004342005.1_ASM434200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:56,648] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:56,651] [INFO] Selected 22 target genomes.
[2024-01-24 12:21:56,652] [INFO] Target genome list was writen to GCF_004342005.1_ASM434200v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:56,661] [INFO] Task started: fastANI
[2024-01-24 12:21:56,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg657873f8-a702-49e9-9cb1-5cfdedff89c8/GCF_004342005.1_ASM434200v1_genomic.fna.gz --refList GCF_004342005.1_ASM434200v1_genomic.fna/target_genomes.txt --output GCF_004342005.1_ASM434200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:15,551] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:15,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64e76f14-ddfb-470b-a1b9-e717f2a759e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:15,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64e76f14-ddfb-470b-a1b9-e717f2a759e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:15,570] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:15,571] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:15,571] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Paracandidimonas soli	strain=DSM 100048	GCA_004342005.1	1917182	1917182	type	True	100.0	1284	1286	95	conclusive
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	79.4218	425	1286	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	79.4131	391	1286	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	79.3769	407	1286	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	79.3416	423	1286	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	79.2715	394	1286	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	79.2333	394	1286	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	79.2021	405	1286	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	79.1754	383	1286	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_1541	GCA_020735925.1	519	519	suspected-type	True	79.165	423	1286	95	below_threshold
Bordetella parapertussis	strain=NCTC5952	GCA_900445785.1	519	519	suspected-type	True	79.1486	415	1286	95	below_threshold
Bordetella parapertussis	strain=FDAARGOS_177	GCA_001525545.2	519	519	suspected-type	True	79.1238	418	1286	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	79.0598	405	1286	95	below_threshold
Achromobacter xylosoxidans	strain=NBRC 15126	GCA_001598595.1	85698	85698	type	True	79.0087	464	1286	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	78.9845	475	1286	95	below_threshold
Achromobacter xylosoxidans	strain=NCTC10807	GCA_001457475.1	85698	85698	type	True	78.9722	475	1286	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	78.9524	403	1286	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	78.9119	467	1286	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	78.77	440	1286	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	78.4929	410	1286	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.1646	218	1286	95	below_threshold
Chromobacterium aquaticum	strain=DSM 19852	GCA_021129195.1	467180	467180	type	True	76.5144	144	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:15,573] [INFO] DFAST Taxonomy check result was written to GCF_004342005.1_ASM434200v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:15,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:15,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:15,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64e76f14-ddfb-470b-a1b9-e717f2a759e1/dqc_reference/checkm_data
[2024-01-24 12:22:15,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:15,614] [INFO] Task started: CheckM
[2024-01-24 12:22:15,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342005.1_ASM434200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342005.1_ASM434200v1_genomic.fna/checkm_input GCF_004342005.1_ASM434200v1_genomic.fna/checkm_result
[2024-01-24 12:22:55,627] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:55,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:55,656] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:55,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:55,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342005.1_ASM434200v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:55,657] [INFO] Task started: Blastn
[2024-01-24 12:22:55,657] [INFO] Running command: blastn -query GCF_004342005.1_ASM434200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64e76f14-ddfb-470b-a1b9-e717f2a759e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342005.1_ASM434200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:57,749] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:57,754] [INFO] Selected 21 target genomes.
[2024-01-24 12:22:57,754] [INFO] Target genome list was writen to GCF_004342005.1_ASM434200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:57,793] [INFO] Task started: fastANI
[2024-01-24 12:22:57,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg657873f8-a702-49e9-9cb1-5cfdedff89c8/GCF_004342005.1_ASM434200v1_genomic.fna.gz --refList GCF_004342005.1_ASM434200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342005.1_ASM434200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:20,323] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:20,346] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:20,346] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004342005.1	s__Paracandidimonas soli	100.0	1284	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paracandidimonas	95.0	98.75	98.75	0.86	0.86	2	conclusive
GCF_014203015.1	s__Castellaniella defragrans	79.3582	408	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.06	98.49	0.94	0.90	4	-
GCF_013416525.1	s__Parapusillimonas granuli	79.3479	422	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002885955.2	s__Achromobacter pulmonis_A	79.3025	473	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	98.97	98.79	0.92	0.89	3	-
GCF_002209565.1	s__Candidimonas nitroreducens	79.2475	401	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306945.1	s__Bordetella pertussis	79.1615	385	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_017356245.1	s__Bordetella_A petrii_D	79.1167	427	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859745.1	s__Achromobacter dolens	79.1035	433	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	99.05	99.03	0.93	0.90	8	-
GCF_902859695.1	s__Achromobacter ruhlandii	79.0401	463	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0063	98.29	97.95	0.91	0.85	19	-
GCF_016127315.1	s__Achromobacter insuavis_A	78.9823	476	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	97.14	97.13	0.90	0.90	4	-
GCF_019166065.1	s__Candidimonas humi	78.9529	403	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261345.1	s__Bordetella_A sp002261345	78.9092	458	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_902859645.1	s__Achromobacter insuavis	78.8793	471	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.6014	99.48	98.86	0.95	0.90	7	-
GCF_002261225.1	s__Bordetella_C sp002261225	78.8535	456	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002119665.1	s__Bordetella_B sp002119665	78.783	438	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416435.1	s__Parapusillimonas sp013416435	78.7798	334	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902859765.1	s__Achromobacter pulmonis	78.7518	441	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.40	99.40	0.96	0.96	2	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	78.6215	388	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003854895.1	s__Pigmentiphaga sp003854895	78.2948	345	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261215.1	s__Bordetella_C sp002261215	78.2414	375	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008119665.1	s__Pigmentiphaga aceris	77.3478	214	1286	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pigmentiphaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:20,348] [INFO] GTDB search result was written to GCF_004342005.1_ASM434200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:20,349] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:20,355] [INFO] DFAST_QC result json was written to GCF_004342005.1_ASM434200v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:20,355] [INFO] DFAST_QC completed!
[2024-01-24 12:23:20,355] [INFO] Total running time: 0h1m39s